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Background  We have developed a rice-based oral cholera vaccine named MucoRice-CTB (Cholera Toxin B-subunit) by using an  Agrobacterium tumefaciens –mediated co-transformation system. To assess the genome-wide effects of this system on the rice genome, we compared the genomes of three selection marker–free MucoRice-CTB lines with those of two wild-type rice lines ( Oryza sativa  L. cv. Nipponbare). Mutation profiles of the transgenic and wild-type genomes were examined by next-generation sequencing (NGS).    Results  Using paired-end short-read sequencing, a total of more than 300 million reads for each line were obtained and mapped onto the rice reference genome. The number and distribution of variants were similar in all five lines: the numbers of line-specific variants ranged from 524 to 842 and corresponding mutation rates ranged from 1.41 × 10 −6  per site to 2.28 × 10 −6  per site. The frequency of guanine-to-thymine and cytosine-to-adenine transversions was higher in MucoRice-CTB lines than in WT lines. The transition-to-transversion ratio was 1.12 in MucoRice-CTB lines and 1.65 in WT lines. Analysis of variant-sharing profiles showed that the variants common to all five lines were the most abundant, and the numbers of line-specific variant for all lines were similar. The numbers of non-synonymous amino acid substitutions in MucoRice-CTB lines (15 to 21) were slightly higher than those in WT lines (7 or 8), whereas the numbers of frame shifts were similar in all five lines.    Conclusions  We conclude that MucoRice-CTB and WT are almost identical at the genomic level and that genome-wide effects caused by the  Agrobacterium -mediated transformation system for marker-free MucoRice-CTB lines were slight. The comparative whole-genome analyses between MucoRice-CTB and WT lines using NGS provides a reliable estimate of genome-wide differences. A similar approach may be applicable to other transgenic rice plants generated by using this  Agrobacterium -mediated transformation system.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-015-1285-y) contains supplementary material, which is available to authorized users.

Comparative whole-genome analyses of selection marker–free rice-based cholera toxin B-subunit vaccine lines and wild-type lines